We have analyzed the antibody response against either AAV2 or canine F.IX (cF.IX) in parental C57BL/6 (B6) and DBA/2 (D2) and 18 strains of B6 × D2 (BXD) recombinant inbred (RI) strains of mice after iv administration of AAV2-(ApoE)4/hAAT-cF.IX. There was a higher anti-AAV2 capsid response in B6 compared to D2 mice, with IgG2b being the major isotype separating the high and low responders in these two strains. In contrast, the antibody response to cF.IX was lower than the response to the AAV2 capsid and was limited to the IgG1 isotype in both strains. Genetic linkage analysis of the IgG2b anti-AAV2 antibody response in BXD RI strains revealed a significant locus at D4Mit164 (29 cM, LRS = 15.3) and two suggestive loci at D6Mit16 (30.5 cM, LRS = 11.2) and D17Mit187 (47.4 cM, LRS = 13.1). Genetic linkage analysis of the IgG1 anti-cF.IX antibody response revealed a suggestive locus at D1Mit218 (67 cM, LRS = 14.1). Significant epistatic interaction was found between two loci (D8Mit45 and D16Mit47; LOD = 6.54) for anti-AAV2 and two other loci (D5Mit348 and D15Mit161; LOD = 7.66) for anti-cF.IX. These results indicate that multiple genetic loci independently regulate the isotype-specific antibody response to the AAV2 capsid and the cF.IX transgene. Copyright © The American Society of Gene Therapy.